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Conserved domains on  [gi|1498198564|gb|RMG53566|]
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bifunctional DNA-formamidopyrimidine glycosylase/DNA-(apurinic or apyrimidinic site) lyase [Chloroflexi bacterium]

Protein Classification

Fpg/Nei family DNA glycosylase( domain architecture ID 11479425)

Fpg/Nei family DNA glycosylase similar to Escherichia coli DNA-formamidopyrimidine glycosylase (Fpg), a DNA repair enzyme that excises oxidized purines from damaged DNA

CATH:  3.20.190.10
EC:  3.2.2.23
Gene Ontology:  GO:0140078|GO:0003684|GO:0008534|GO:0008270|GO:0006284
PubMed:  21486746|14607836
SCOP:  4000303

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK01103 PRK01103
bifunctional DNA-formamidopyrimidine glycosylase/DNA-(apurinic or apyrimidinic site) lyase;
1-271 1.00e-149

bifunctional DNA-formamidopyrimidine glycosylase/DNA-(apurinic or apyrimidinic site) lyase;


:

Pssm-ID: 234899 [Multi-domain]  Cd Length: 274  Bit Score: 419.49  E-value: 1.00e-149
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1498198564   1 MPELPEVETVARSLAPQLQGRTITGlAKLDWPKMLTPSPDEFAALIAGRRIEAIGRRAKWLLLSLDGEWTLAIHLRMSGQ 80
Cdd:PRK01103    1 MPELPEVETVRRGLEPHLVGKTITR-VEVRRPKLRWPVPEDFAERLSGQTILAVGRRGKYLLLDLDDGGTLISHLGMSGS 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1498198564  81 LLVAEPETSEARHVHFALDLDNGRRLIFNDQRKFGRVHLLDRQGLAALD--AVHGPEPLAADFTPSALAERLQNRRAPIK 158
Cdd:PRK01103   80 LRLLPEDTPPEKHDHVDFVLDDGTVLRYNDPRRFGAMLLTPKGDLEAHPllAHLGPEPLSDAFDGEYLAAKLRKKKTAIK 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1498198564 159 ALLLDQHLIAGIGNIYANEALWLARIHPLTPGAMLTPEQINELHHAIRHVLQEAITNQGSSLRNYRDGYGRQGTQQEHFN 238
Cdd:PRK01103  160 PALLDQTVVVGVGNIYADEALFRAGIHPERPAGSLSRAEAERLVDAIKAVLAEAIEQGGTTLRDYVNADGKPGYFQQSLQ 239

                         250       260       270
                  ....*....|....*....|....*....|...
gi 1498198564 239 VYDRAGEPCPRCQSTIERIVVAQRSTYFCPTCQ 271
Cdd:PRK01103  240 VYGREGEPCRRCGTPIEKIKQGGRSTFFCPRCQ 272
 
Name Accession Description Interval E-value
PRK01103 PRK01103
bifunctional DNA-formamidopyrimidine glycosylase/DNA-(apurinic or apyrimidinic site) lyase;
1-271 1.00e-149

bifunctional DNA-formamidopyrimidine glycosylase/DNA-(apurinic or apyrimidinic site) lyase;


Pssm-ID: 234899 [Multi-domain]  Cd Length: 274  Bit Score: 419.49  E-value: 1.00e-149
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1498198564   1 MPELPEVETVARSLAPQLQGRTITGlAKLDWPKMLTPSPDEFAALIAGRRIEAIGRRAKWLLLSLDGEWTLAIHLRMSGQ 80
Cdd:PRK01103    1 MPELPEVETVRRGLEPHLVGKTITR-VEVRRPKLRWPVPEDFAERLSGQTILAVGRRGKYLLLDLDDGGTLISHLGMSGS 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1498198564  81 LLVAEPETSEARHVHFALDLDNGRRLIFNDQRKFGRVHLLDRQGLAALD--AVHGPEPLAADFTPSALAERLQNRRAPIK 158
Cdd:PRK01103   80 LRLLPEDTPPEKHDHVDFVLDDGTVLRYNDPRRFGAMLLTPKGDLEAHPllAHLGPEPLSDAFDGEYLAAKLRKKKTAIK 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1498198564 159 ALLLDQHLIAGIGNIYANEALWLARIHPLTPGAMLTPEQINELHHAIRHVLQEAITNQGSSLRNYRDGYGRQGTQQEHFN 238
Cdd:PRK01103  160 PALLDQTVVVGVGNIYADEALFRAGIHPERPAGSLSRAEAERLVDAIKAVLAEAIEQGGTTLRDYVNADGKPGYFQQSLQ 239

                         250       260       270
                  ....*....|....*....|....*....|...
gi 1498198564 239 VYDRAGEPCPRCQSTIERIVVAQRSTYFCPTCQ 271
Cdd:PRK01103  240 VYGREGEPCRRCGTPIEKIKQGGRSTFFCPRCQ 272
Nei COG0266
Formamidopyrimidine-DNA glycosylase [Replication, recombination and repair];
2-271 9.11e-139

Formamidopyrimidine-DNA glycosylase [Replication, recombination and repair];


Pssm-ID: 440036 [Multi-domain]  Cd Length: 272  Bit Score: 391.80  E-value: 9.11e-139
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1498198564   2 PELPEVETVARSLAPQLQGRTITGlAKLDWPKMLTPSPDEFAALIAGRRIEAIGRRAKWLLLSLDGEWTLAIHLRMSGQL 81
Cdd:COG0266     1 PELPEVETVRRGLAPALVGRTITR-VEVRSPRLRFPVPEDFAARLTGRRITAVERRGKYLLLELDGGLTLLIHLGMSGRL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1498198564  82 LVAEPETSEARHVHFALDLDNGRRLIFNDQRKFGRVHLLDRQGLAALDAVH--GPEPLAADFTPSALAERLQNRRAPIKA 159
Cdd:COG0266    80 RVVPPGEPPEKHDHVRLVLDDGTELRFADPRRFGALELLTPDELEVHPLLArlGPEPLDPDFDPEYLAARLRRRRRPIKA 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1498198564 160 LLLDQHLIAGIGNIYANEALWLARIHPLTPGAMLTPEQINELHHAIRHVLQEAITNQGSSLRNYRDGYGRQGTQQEHFNV 239
Cdd:COG0266   160 LLLDQSVVAGVGNIYADEALFRAGIHPLRPAGSLSRAELERLAAAIREVLREAIEAGGTTLRDYVNADGEPGYFQQRLYV 239

                         250       260       270
                  ....*....|....*....|....*....|..
gi 1498198564 240 YDRAGEPCPRCQSTIERIVVAQRSTYFCPTCQ 271
Cdd:COG0266   240 YGREGEPCPRCGTPIERIVLGGRSTYYCPRCQ 271
fpg TIGR00577
DNA-formamidopyrimidine glycosylase; All proteins in the FPG family with known functions are ...
 2-271 7.28e-105

DNA-formamidopyrimidine glycosylase; All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273150 [Multi-domain]  Cd Length: 272  Bit Score: 305.76  E-value: 7.28e-105
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1498198564   2 PELPEVETVARSLAPQLQGRTITGL-AKLDWPKMLTPSPDEFAALIAGRRIEAIGRRAKWLLLSLDGEWtLAIHLRMSGQ 80
Cdd:TIGR00577   1 PELPEVETVRRGLEPLVLGKTIKSVeVVLRNPVLRPAGSEDLQKRLLGQTILSIQRRGKYLLFELDDGA-LVSHLRMEGK 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1498198564  81 LLVAEPETSEARHVHFALDLDNGRRLIFNDQRKFGRVHLLDR-QGLAALDAVH-GPEPLAADFTPSALAERLQNRRAPIK 158
Cdd:TIGR00577  80 YRLEAVPDAPDKHDHVDFLFDDGTELRYHDPRRFGTWLLLDRgQVENIPLLAKlGPEPLSEDFTAEYLFEKLAKSKRKIK 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1498198564 159 ALLLDQHLIAGIGNIYANEALWLARIHPLTPGAMLTPEQINELHHAIRHVLQEAITNQGSSLRNYRDGYGRQGT-QQEHF 237
Cdd:TIGR00577 160 TALLDQRLVAGIGNIYADEVLFRAGIHPERLASSLSKEECELLHRAIKEVLRKAIEMGGTTIRDFSQSDGHNGYfQQELQ 239

                         250       260       270
                  ....*....|....*....|....*....|....
gi 1498198564 238 nVYDRAGEPCPRCQSTIERIVVAQRSTYFCPTCQ 271
Cdd:TIGR00577 240 -VYGRKGEPCRRCGTTIEKEKVGGRGTHFCPQCQ 272
EcFpg-like_N cd08966
N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; This ...
 2-121 7.59e-55

N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; This family contains the N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases. It belongs to the FpgNei_N, [N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII)] domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. They initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycosylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. Escherichia coli Fpg mainly recognizes and excises damaged purines such as 8-oxo-7,8-dihydroguanine (8-oxoG) and 2,6-diamino-4-hydroxy-5-formamidopyrimidine (FapyG). It is bifunctional, having both a DNA glycosylase (recognition activity) and a AP lyase activity. In addition to this EcFpg-like_N domain, enzymes belonging to this family contain a helix-two turn-helix (H2TH) domain and a zinc-finger motif, which also contribute residues to the active site.


Pssm-ID: 176800  Cd Length: 120  Bit Score: 173.07  E-value: 7.59e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1498198564   2 PELPEVETVARSLAPQLQGRTITGLAKLDWPKMLTPSPDEFAALIAGRRIEAIGRRAKWLLLSLDGEWTLAIHLRMSGQL 81
Cdd:cd08966     1 PELPEVETVRRGLAPHLVGRRIEDVEVRRPKLRRPPDPEEFAERLVGRRITGVERRGKYLLFELDDGLVLVIHLGMTGRL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1498198564  82 LVAEPETSEARHVHFALDLDNGRRLIFNDQRKFGRVHLLD 121
Cdd:cd08966    81 LVVPPDEPPEKHDHVIFELDDGRELRFNDPRRFGTLLLVP 120
Fapy_DNA_glyco pfam01149
Formamidopyrimidine-DNA glycosylase N-terminal domain; Formamidopyrimidine-DNA glycosylase ...
 1-117 1.45e-49

Formamidopyrimidine-DNA glycosylase N-terminal domain; Formamidopyrimidine-DNA glycosylase (Fpg) is a DNA repair enzyme that excises oxidized purines from damaged DNA. This family is the N-terminal domain contains eight beta-strands, forming a beta-sandwich with two alpha-helices parallel to its edges.


Pssm-ID: 460082  Cd Length: 116  Bit Score: 159.59  E-value: 1.45e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1498198564   1 MPELPEVETVARSLAPQLQGRTITGLAKLDWPKMLTPSPDEFAALIAGRRIEAIGRRAKWLLLSLDGEWTLAIHLRMSGQ 80
Cdd:pfam01149   1 MPELPEVETVRRGLRRHLVGKTIASVEVLDDKNLRGPSPEEFAAALTGRKVTSVGRRGKYLLLELDSGGHLVVHLGMTGW 80

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1498198564  81 LLVAEPETsEARHVHFALDLDNGRRLIFNDQRKFGRV 117
Cdd:pfam01149  81 LLIKTEEW-PPKHDHVRLELDDGRELRFTDPRRFGRV 116
Fapy_DNA_glyco smart00898
Formamidopyrimidine-DNA glycosylase N-terminal domain; This entry represents the catalytic ...
 2-118 7.94e-45

Formamidopyrimidine-DNA glycosylase N-terminal domain; This entry represents the catalytic domain of DNA glycosylase/AP lyase enzymes, which are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Most damage to bases in DNA is repaired by the base excision repair pathway. These enzymes are primarily from bacteria, and have both DNA glycosylase activity and AP lyase activity. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; ) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; ). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes. Fpg binds one ion of zinc at the C-terminus, which contains four conserved and essential cysteines.. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine. These protein contains three structural domains: an N-terminal catalytic core domain, a central helix-two turn-helix (H2TH) module and a C-terminal zinc finger (see PDB:1K82). The N-terminal catalytic domain and the C-terminal zinc finger straddle the DNA with the long axis of the protein oriented roughly orthogonal to the helical axis of the DNA. Residues that contact DNA are located in the catalytic domain and in a beta-hairpin loop formed by the zinc finger.


Pssm-ID: 214895 [Multi-domain]  Cd Length: 115  Bit Score: 147.33  E-value: 7.94e-45
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1498198564    2 PELPEVETVARSLAPQLQGRTITGlAKLDWPKMLTpSPDEFAALIAGRRIEAIGRRAKWLLLSLDGEWTLAIHLRMSGQL 81
Cdd:smart00898   1 PELPEVETVRRGLAPALAGRTITR-VEVVRPPQLR-FPDEFAAALSGRTITSVRRRGKYLLLRLLGGLTLVVHLGMSGSL 78

                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 1498198564   82 LVAEPETSEARHVHFALDLDNGRRLIFNDQRKFGRVH 118
Cdd:smart00898  79 RVVPAGTPPPKHDHVRLVLDDGTELRFNDPRRFGAVR 115
 
Name Accession Description Interval E-value
PRK01103 PRK01103
bifunctional DNA-formamidopyrimidine glycosylase/DNA-(apurinic or apyrimidinic site) lyase;
1-271 1.00e-149

bifunctional DNA-formamidopyrimidine glycosylase/DNA-(apurinic or apyrimidinic site) lyase;


Pssm-ID: 234899 [Multi-domain]  Cd Length: 274  Bit Score: 419.49  E-value: 1.00e-149
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1498198564   1 MPELPEVETVARSLAPQLQGRTITGlAKLDWPKMLTPSPDEFAALIAGRRIEAIGRRAKWLLLSLDGEWTLAIHLRMSGQ 80
Cdd:PRK01103    1 MPELPEVETVRRGLEPHLVGKTITR-VEVRRPKLRWPVPEDFAERLSGQTILAVGRRGKYLLLDLDDGGTLISHLGMSGS 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1498198564  81 LLVAEPETSEARHVHFALDLDNGRRLIFNDQRKFGRVHLLDRQGLAALD--AVHGPEPLAADFTPSALAERLQNRRAPIK 158
Cdd:PRK01103   80 LRLLPEDTPPEKHDHVDFVLDDGTVLRYNDPRRFGAMLLTPKGDLEAHPllAHLGPEPLSDAFDGEYLAAKLRKKKTAIK 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1498198564 159 ALLLDQHLIAGIGNIYANEALWLARIHPLTPGAMLTPEQINELHHAIRHVLQEAITNQGSSLRNYRDGYGRQGTQQEHFN 238
Cdd:PRK01103  160 PALLDQTVVVGVGNIYADEALFRAGIHPERPAGSLSRAEAERLVDAIKAVLAEAIEQGGTTLRDYVNADGKPGYFQQSLQ 239

                         250       260       270
                  ....*....|....*....|....*....|...
gi 1498198564 239 VYDRAGEPCPRCQSTIERIVVAQRSTYFCPTCQ 271
Cdd:PRK01103  240 VYGREGEPCRRCGTPIEKIKQGGRSTFFCPRCQ 272
Nei COG0266
Formamidopyrimidine-DNA glycosylase [Replication, recombination and repair];
2-271 9.11e-139

Formamidopyrimidine-DNA glycosylase [Replication, recombination and repair];


Pssm-ID: 440036 [Multi-domain]  Cd Length: 272  Bit Score: 391.80  E-value: 9.11e-139
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1498198564   2 PELPEVETVARSLAPQLQGRTITGlAKLDWPKMLTPSPDEFAALIAGRRIEAIGRRAKWLLLSLDGEWTLAIHLRMSGQL 81
Cdd:COG0266     1 PELPEVETVRRGLAPALVGRTITR-VEVRSPRLRFPVPEDFAARLTGRRITAVERRGKYLLLELDGGLTLLIHLGMSGRL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1498198564  82 LVAEPETSEARHVHFALDLDNGRRLIFNDQRKFGRVHLLDRQGLAALDAVH--GPEPLAADFTPSALAERLQNRRAPIKA 159
Cdd:COG0266    80 RVVPPGEPPEKHDHVRLVLDDGTELRFADPRRFGALELLTPDELEVHPLLArlGPEPLDPDFDPEYLAARLRRRRRPIKA 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1498198564 160 LLLDQHLIAGIGNIYANEALWLARIHPLTPGAMLTPEQINELHHAIRHVLQEAITNQGSSLRNYRDGYGRQGTQQEHFNV 239
Cdd:COG0266   160 LLLDQSVVAGVGNIYADEALFRAGIHPLRPAGSLSRAELERLAAAIREVLREAIEAGGTTLRDYVNADGEPGYFQQRLYV 239

                         250       260       270
                  ....*....|....*....|....*....|..
gi 1498198564 240 YDRAGEPCPRCQSTIERIVVAQRSTYFCPTCQ 271
Cdd:COG0266   240 YGREGEPCPRCGTPIERIVLGGRSTYYCPRCQ 271
fpg TIGR00577
DNA-formamidopyrimidine glycosylase; All proteins in the FPG family with known functions are ...
 2-271 7.28e-105

DNA-formamidopyrimidine glycosylase; All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273150 [Multi-domain]  Cd Length: 272  Bit Score: 305.76  E-value: 7.28e-105
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1498198564   2 PELPEVETVARSLAPQLQGRTITGL-AKLDWPKMLTPSPDEFAALIAGRRIEAIGRRAKWLLLSLDGEWtLAIHLRMSGQ 80
Cdd:TIGR00577   1 PELPEVETVRRGLEPLVLGKTIKSVeVVLRNPVLRPAGSEDLQKRLLGQTILSIQRRGKYLLFELDDGA-LVSHLRMEGK 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1498198564  81 LLVAEPETSEARHVHFALDLDNGRRLIFNDQRKFGRVHLLDR-QGLAALDAVH-GPEPLAADFTPSALAERLQNRRAPIK 158
Cdd:TIGR00577  80 YRLEAVPDAPDKHDHVDFLFDDGTELRYHDPRRFGTWLLLDRgQVENIPLLAKlGPEPLSEDFTAEYLFEKLAKSKRKIK 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1498198564 159 ALLLDQHLIAGIGNIYANEALWLARIHPLTPGAMLTPEQINELHHAIRHVLQEAITNQGSSLRNYRDGYGRQGT-QQEHF 237
Cdd:TIGR00577 160 TALLDQRLVAGIGNIYADEVLFRAGIHPERLASSLSKEECELLHRAIKEVLRKAIEMGGTTIRDFSQSDGHNGYfQQELQ 239

                         250       260       270
                  ....*....|....*....|....*....|....
gi 1498198564 238 nVYDRAGEPCPRCQSTIERIVVAQRSTYFCPTCQ 271
Cdd:TIGR00577 240 -VYGRKGEPCRRCGTTIEKEKVGGRGTHFCPQCQ 272
PRK13945 PRK13945
formamidopyrimidine-DNA glycosylase; Provisional
 1-271 9.68e-82

formamidopyrimidine-DNA glycosylase; Provisional


Pssm-ID: 184410 [Multi-domain]  Cd Length: 282  Bit Score: 247.53  E-value: 9.68e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1498198564   1 MPELPEVETVARSLAPQLQGRTITGLAKLDWPKMLTP-SPDEFAALIAGRRIEAIGRRAKWLLLSLDGEW-----TLAIH 74
Cdd:PRK13945    1 MPELPEVETVRRGLEQLLLNFIIKGVEVLLERTIASPgGVEEFIKGLKGSLIGQWQRRGKYLLASLKKEGsenagWLGVH 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1498198564  75 LRMSGQLLVAEPETSEARHVHFALDLDNGRRLIFNDQRKFGRVHLL--DRQ------GLAALdavhGPEPLAADFTPSAL 146
Cdd:PRK13945   81 LRMTGQFLWVEQSTPPCKHTRVRLFFEKNQELRFVDIRSFGQMWWVppGVSpesiitGLQKL----GPEPFSPEFSVEYL 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1498198564 147 AERLQNRRAPIKALLLDQHLIAGIGNIYANEALWLARIHPLTPGAMLTPEQINELHHAIRHVLQEAITNQGSSLRNYRDG 226
Cdd:PRK13945  157 KKKLKKRTRSIKTALLDQSIVAGIGNIYADESLFKAGIHPTTPAGQLKKKQLERLREAIIEVLKTSIGAGGTTFSDFRDL 236

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*
gi 1498198564 227 YGRQGTQQEHFNVYDRAGEPCPRCQSTIERIVVAQRSTYFCPTCQ 271
Cdd:PRK13945  237 EGVNGNYGGQAWVYRRTGKPCRKCGTPIERIKLAGRSTHWCPNCQ 281
PRK14811 PRK14811
formamidopyrimidine-DNA glycosylase; Provisional
 1-271 8.05e-74

formamidopyrimidine-DNA glycosylase; Provisional


Pssm-ID: 184831 [Multi-domain]  Cd Length: 269  Bit Score: 226.99  E-value: 8.05e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1498198564   1 MPELPEVETVARSLAPQLQGRTITGLAKLDwpkmltPSPDEFAALIAGRRIEAIGRRAKWLLLSLDGEWTLAIHLRMSGQ 80
Cdd:PRK14811    1 MPELPEVETTRRKLEPLLLGQTIQQVVHDD------PARYRNTELAEGRRVLGLSRRGKYLLLHLPHDLELIVHLGMTGG 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1498198564  81 LlvaepETSEARHVHFALDLDnGRRLIFNDQRKFGRVHLLDRQGLAALD--AVHGPEPLAADFTPSALAERLQNRRaPIK 158
Cdd:PRK14811   75 F-----RLEPGPHTRVTLELP-GRTLYFTDPRRFGKWWVVRAGDYREIPllARMGPEPLSDDFTEPEFVRALATAR-PVK 147

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1498198564 159 ALLLDQHLIAGIGNIYANEALWLARIHPLTPGAMLTPEQINELHHAIRHVLQEAITNQGSSL--RNYRDGYGRQGTQQEH 236
Cdd:PRK14811  148 PWLLSQKPVAGVGNIYADESLWRARIHPARPATSLKAPEARRLYRAIREVMAEAVEAGGSTLsdGSYRQPDGEPGGFQFQ 227

                         250       260       270
                  ....*....|....*....|....*....|....*
gi 1498198564 237 FNVYDRAGEPCPRCQSTIERIVVAQRSTYFCPTCQ 271
Cdd:PRK14811  228 HAVYGREGQPCPRCGTPIEKIVVGGRGTHFCPQCQ 262
PRK14810 PRK14810
formamidopyrimidine-DNA glycosylase; Provisional
 1-271 4.60e-71

formamidopyrimidine-DNA glycosylase; Provisional


Pssm-ID: 173271 [Multi-domain]  Cd Length: 272  Bit Score: 219.78  E-value: 4.60e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1498198564   1 MPELPEVETVARSLAPQLQGRTITGLAKLDWPKMLTPSPDEFAALIAGRRIEAIGRRAKWLLLSLDG----EWTLAIHLR 76
Cdd:PRK14810    1 MPELPEVETVARGLAPRAAGRRIATAEFRNLRIPRKGDPDLMAARLAGRKILSVKRVGKHIVADLEGpgepRGQWIIHLG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1498198564  77 MSGQLLVAEPETSEARHVHFALDLDNGRRLIFNDQRKFGRVHLldRQGLAALDAVHGPEPLaaDFTPSALAERLQNRRAP 156
Cdd:PRK14810   81 MTGKLLLGGPDTPSPKHTHAVLTLSSGKELRFVDSRQFGCIEY--SEAFPKRFARPGPEPL--EISFEDFAALFRGRKTR 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1498198564 157 IKALLLDQHLIAGIGNIYANEALWLARIHPLTPGAMLTPEQINELHHAIRHVLQEAITNQGSSLRNYRDGYGRQGTQQEH 236
Cdd:PRK14810  157 IKSALLNQTLLRGVGNIYADEALFRAGIRPQRLASSLSRERLRKLHDAIGEVLREAIELGGSSVSDYVDAEGRSGFFQLS 236

                         250       260       270
                  ....*....|....*....|....*....|....*
gi 1498198564 237 FNVYDRAGEPCPRCQSTIERIVVAQRSTYFCPTCQ 271
Cdd:PRK14810  237 HRVYQRTGEPCLNCKTPIRRVVVAGRSSHYCPHCQ 271
EcFpg-like_N cd08966
N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; This ...
 2-121 7.59e-55

N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; This family contains the N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases. It belongs to the FpgNei_N, [N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII)] domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. They initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycosylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. Escherichia coli Fpg mainly recognizes and excises damaged purines such as 8-oxo-7,8-dihydroguanine (8-oxoG) and 2,6-diamino-4-hydroxy-5-formamidopyrimidine (FapyG). It is bifunctional, having both a DNA glycosylase (recognition activity) and a AP lyase activity. In addition to this EcFpg-like_N domain, enzymes belonging to this family contain a helix-two turn-helix (H2TH) domain and a zinc-finger motif, which also contribute residues to the active site.


Pssm-ID: 176800  Cd Length: 120  Bit Score: 173.07  E-value: 7.59e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1498198564   2 PELPEVETVARSLAPQLQGRTITGLAKLDWPKMLTPSPDEFAALIAGRRIEAIGRRAKWLLLSLDGEWTLAIHLRMSGQL 81
Cdd:cd08966     1 PELPEVETVRRGLAPHLVGRRIEDVEVRRPKLRRPPDPEEFAERLVGRRITGVERRGKYLLFELDDGLVLVIHLGMTGRL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1498198564  82 LVAEPETSEARHVHFALDLDNGRRLIFNDQRKFGRVHLLD 121
Cdd:cd08966    81 LVVPPDEPPEKHDHVIFELDDGRELRFNDPRRFGTLLLVP 120
Fapy_DNA_glyco pfam01149
Formamidopyrimidine-DNA glycosylase N-terminal domain; Formamidopyrimidine-DNA glycosylase ...
 1-117 1.45e-49

Formamidopyrimidine-DNA glycosylase N-terminal domain; Formamidopyrimidine-DNA glycosylase (Fpg) is a DNA repair enzyme that excises oxidized purines from damaged DNA. This family is the N-terminal domain contains eight beta-strands, forming a beta-sandwich with two alpha-helices parallel to its edges.


Pssm-ID: 460082  Cd Length: 116  Bit Score: 159.59  E-value: 1.45e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1498198564   1 MPELPEVETVARSLAPQLQGRTITGLAKLDWPKMLTPSPDEFAALIAGRRIEAIGRRAKWLLLSLDGEWTLAIHLRMSGQ 80
Cdd:pfam01149   1 MPELPEVETVRRGLRRHLVGKTIASVEVLDDKNLRGPSPEEFAAALTGRKVTSVGRRGKYLLLELDSGGHLVVHLGMTGW 80

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1498198564  81 LLVAEPETsEARHVHFALDLDNGRRLIFNDQRKFGRV 117
Cdd:pfam01149  81 LLIKTEEW-PPKHDHVRLELDDGRELRFTDPRRFGRV 116
Fapy_DNA_glyco smart00898
Formamidopyrimidine-DNA glycosylase N-terminal domain; This entry represents the catalytic ...
 2-118 7.94e-45

Formamidopyrimidine-DNA glycosylase N-terminal domain; This entry represents the catalytic domain of DNA glycosylase/AP lyase enzymes, which are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Most damage to bases in DNA is repaired by the base excision repair pathway. These enzymes are primarily from bacteria, and have both DNA glycosylase activity and AP lyase activity. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; ) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; ). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes. Fpg binds one ion of zinc at the C-terminus, which contains four conserved and essential cysteines.. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine. These protein contains three structural domains: an N-terminal catalytic core domain, a central helix-two turn-helix (H2TH) module and a C-terminal zinc finger (see PDB:1K82). The N-terminal catalytic domain and the C-terminal zinc finger straddle the DNA with the long axis of the protein oriented roughly orthogonal to the helical axis of the DNA. Residues that contact DNA are located in the catalytic domain and in a beta-hairpin loop formed by the zinc finger.


Pssm-ID: 214895 [Multi-domain]  Cd Length: 115  Bit Score: 147.33  E-value: 7.94e-45
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1498198564    2 PELPEVETVARSLAPQLQGRTITGlAKLDWPKMLTpSPDEFAALIAGRRIEAIGRRAKWLLLSLDGEWTLAIHLRMSGQL 81
Cdd:smart00898   1 PELPEVETVRRGLAPALAGRTITR-VEVVRPPQLR-FPDEFAAALSGRTITSVRRRGKYLLLRLLGGLTLVVHLGMSGSL 78

                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 1498198564   82 LVAEPETSEARHVHFALDLDNGRRLIFNDQRKFGRVH 118
Cdd:smart00898  79 RVVPAGTPPPKHDHVRLVLDDGTELRFNDPRRFGAVR 115
H2TH pfam06831
Formamidopyrimidine-DNA glycosylase H2TH domain; Formamidopyrimidine-DNA glycosylase (Fpg) is ...
 133-220 2.12e-35

Formamidopyrimidine-DNA glycosylase H2TH domain; Formamidopyrimidine-DNA glycosylase (Fpg) is a DNA repair enzyme that excises oxidized purines from damaged DNA. This family is the central domain containing the DNA-binding helix-two turn-helix domain.


Pssm-ID: 399664 [Multi-domain]  Cd Length: 89  Bit Score: 122.40  E-value: 2.12e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1498198564 133 GPEPLAADFTPSALAERLQNRRAPIKALLLDQHLIAGIGNIYANEALWLARIHPLTPGAMLTPEQINELHHAIRHVLQEA 212
Cdd:pfam06831   2 GPEPLSEDFTVDYFAERLAKKKRPIKTALLDQTLVAGLGNIYADEVLFRAGIHPERLANSLSKEECELLHQAIKAVLQEA 81


                  ....*...
gi 1498198564 213 ITNQGSSL 220
Cdd:pfam06831  82 IEMGGGGI 89
PRK10445 PRK10445
endonuclease VIII; Provisional
 1-272 1.33e-33

endonuclease VIII; Provisional


Pssm-ID: 182467 [Multi-domain]  Cd Length: 263  Bit Score: 122.83  E-value: 1.33e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1498198564   1 MPELPEVETVARSLAPQLQGRTITGLakldWpkMLTPSPDEFAALIAGRRIEAIGRRAKWLLLSLDGEWTLAIHLRMSGQ 80
Cdd:PRK10445    1 MPEGPEIRRAADNLEAAIKGKPLTDV----W--FAFPQLKPYESQLIGQRVTHIETRGKALLTHFSNGLTLYSHNQLYGV 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1498198564  81 LLVA----EPETSEARHVHfaldLDNGRRLIF----NDqrkfgrVHLLDRQGLAA---LDAVhGPEPLAADFTPSALAER 149
Cdd:PRK10445   75 WRVVdtgeEPQTTRVLRVR----LQTADKTILlysaSD------IEMLTPEQLTThpfLQRV-GPDVLDPNLTPEQVKER 143

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1498198564 150 LQN---RRAPIKALLLDQHLIAGIGNIYANEALWLARIHPLTPGAMLTPEQINELHHAIRHVLQEAITNQGSSLRNYRDG 226
Cdd:PRK10445  144 LLSprfRNRQFSGLLLDQAFLAGLGNYLRVEILWQAGLTPQHKAKDLNEAQLDALAHALLDIPRLSYATRGQVDENKHHG 223

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*.
gi 1498198564 227 ygrqgtQQEHFNVYDRAGEPCPRCQSTIERIVVAQRSTYFCPTCQI 272
Cdd:PRK10445  224 ------ALFRFKVFHRDGEACERCGGIIEKTTLSSRPFYWCPGCQK 263
FpgNei_N cd08773
N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) ...
 2-119 1.80e-29

N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) base-excision repair DNA glycosylases; DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. These enzymes initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycolsylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. The FpgNei DNA glycosylases represent one of the two structural superfamilies of DNA glycosylases that recognize oxidized bases (the other is the HTH-GPD superfamily exemplified by Escherichia coli Nth). Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. One exception is mouse Nei-like glycosylase 3 (Neil3) which forms a Schiff base intermediate via its N-terminal valine. In addition to this FpgNei_N domain, FpgNei proteins have a helix-two-turn-helix (H2TH) domain and a zinc (or zincless)-finger motif which also contribute residues to the active site. FpgNei DNA glycosylases have a broad substrate specificity. They are bifunctional, in addition to the glycosylase (recognition) activity, they have a lyase (cleaving) activity on the phosphodiester backbone of the DNA at the AP site. This superfamily includes eukaryotic, bacterial, and viral proteins.


Pssm-ID: 176798  Cd Length: 117  Bit Score: 107.83  E-value: 1.80e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1498198564   2 PELPEVETVARSLAPQLQGRTITGlAKLDWPKMLTPSPDEFAALIAGRRIEAIGRRAKWLLLSLDGEWTLAIHLRMSGQL 81
Cdd:cd08773     1 PELPEVELLRRKLRRALKGKRVTR-VEVSDPRRLFTPAAELAAALIGRRVRGAERRGKYLLLELSGGPWLVIHLGMTGRL 79

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1498198564  82 LVAEPETSEARHVHFALDLDNGRRLIFNDQRKFGRVHL 119
Cdd:cd08773    80 RVCPEGEPPPKHDRLVLRLANGSQLRFTDPRKFGRVEL 117
PF_Nei_N cd08972
N-terminal domain of the plant and fungal Nei and related proteins; This family contains the ...
 1-120 9.78e-20

N-terminal domain of the plant and fungal Nei and related proteins; This family contains the N-terminal domain of plant and Fungi Nei and related proteins. It belongs to the FpgNei_N, [N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII)] domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. They initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycosylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. The plant and fungal FpgNei glycosylases prefer the oxidized pyrimidines spiroiminodihydantoin (Sp), guanidinohydantoin (Gh) over 8-oxoguanine in double stranded oligonucleotides and also show weak activity on single stranded DNA. In addition to this domain, enzymes belonging to this family contain a helix-two turn-helix (H2TH) domain and a characteristic zincless finger motif. They share a common ancestor not shared with other eukaryotic members of the FpgNei family.


Pssm-ID: 176806  Cd Length: 137  Bit Score: 82.74  E-value: 9.78e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1498198564   1 MPELPEVETVARSLAPQLQGRTITGLAKLDWPKMLTP-SPDEFAALIAGRRIEAIGRRAK--WLLLSLDGEWtLAIHLRM 77
Cdd:cd08972     1 MPELPEVERARRLLEEHCLGKKITKVDAQDDDKVFGGvTPGAFQKALLGRTITSAHRKGKyfWLTLDGDAPV-PVMHFGM 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1498198564  78 SGQLLVAEPETSEA---------------RHVHFALDLDNGRRLIFNDQRKFGRVHLL 120
Cdd:cd08972    80 TGAISIKGVKTIYYkmlrppkeedqtwppRFYKFVLTLEDGTELAFTDPRRLGRVRLV 137
BaFpgNei_N_4 cd08976
Uncharacterized bacterial subgroup of the N-terminal domain of Fpg (formamidopyrimidine-DNA ...
 2-119 2.58e-16

Uncharacterized bacterial subgroup of the N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) base-excision repair DNA glycosylases; This family is an uncharacterized bacterial subgroup of the FpgNei_N domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. They initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycosylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. This N-terminal proline is conserved in this family. Escherichia coli Fpg prefers 8-oxo-7,8-dihydroguanine (8-oxoG) and oxidized purines and Escherichia coli Nei recognizes oxidized pyrimidines. However, neither Escherichia coli Fpg or Nei belong to this family. In addition to this BaFpgNei_N_4 domain, most enzymes belonging to this family contain a helix-two turn-helix (H2TH) domain and a zinc-finger motif.


Pssm-ID: 176810  Cd Length: 117  Bit Score: 73.15  E-value: 2.58e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1498198564   2 PELPEVETVARSLAPQLQGRTITGLAKLDwPKMLTPSPDEFAALIAGRRIEAIGRRAKWLLLSLDGEWTLAIHLRMSGQL 81
Cdd:cd08976     1 PELPEVEVQKQYLERTSLHRKIVEVEVGD-DKILGEPKATLREVLEGRTFTETHRIGKYLFLKTKEGGWLVMHFGMTGKL 79

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1498198564  82 LVAEPETSEARHVHFALDLDNGRRLIFNDQRKFGRVHL 119
Cdd:cd08976    80 DYYPDDEDPPKHARLLLHFEDGFRLAFECPRKFGRVRL 117
BaFpgNei_N_1 cd08973
Uncharacterized bacterial subgroup of the N-terminal domain of Fpg (formamidopyrimidine-DNA ...
 1-101 4.84e-14

Uncharacterized bacterial subgroup of the N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) base-excision repair DNA glycosylases; This family is an uncharacterized bacterial subgroup of the FpgNei_N domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. They initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycosylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. This N-terminal proline is conserved in this family. Escherichia coli Fpg prefers 8-oxo-7,8-dihydroguanine (8-oxoG) and oxidized purines and Escherichia coli Nei recognizes oxidized pyrimidines. However, neither Escherichia coli Fpg or Nei belong to this family. In addition to this BaFpgNei_N_1 domain, enzymes belonging to this family contain a helix-two turn-helix (H2TH) domain and a zinc-finger motif.


Pssm-ID: 176807  Cd Length: 122  Bit Score: 67.27  E-value: 4.84e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1498198564   1 MPELPEVETVARSLAPQLQGRTITGLaKLDWPKMLTPsPDEFAALIAGRRIEAIGRRAKWLLLSLDGEWTLAIHLRMSGQ 80
Cdd:cd08973     1 MPELPEVEVYAENLERRLTGKTITRV-ELASKSLLVT-PDPPLEALEGRTVTGVRRHGKRLDFEFDNGLHLVLHLMLAGW 78

                          90       100
                  ....*....|....*....|..
gi 1498198564  81 L-LVAEPETSEARHVHFALDLD 101
Cdd:cd08973    79 LyWTEAGALLPGKKGPIALRFE 100
zf-FPG_IleRS pfam06827
Zinc finger found in FPG and IleRS; This zinc binding domain is found at the C-terminus of ...
 244-271 6.68e-12

Zinc finger found in FPG and IleRS; This zinc binding domain is found at the C-terminus of isoleucyl tRNA synthetase and the enzyme Formamidopyrimidine-DNA glycosylase EC:3.2.2.23.


Pssm-ID: 429140 [Multi-domain]  Cd Length: 28  Bit Score: 58.75  E-value: 6.68e-12
                          10        20
                  ....*....|....*....|....*...
gi 1498198564 244 GEPCPRCQSTIERIVVAQRSTYFCPTCQ 271
Cdd:pfam06827   1 GEKCPRCWTYIEKVGVGGRSTYFCPRCQ 28
AcNei2_N cd08971
N-terminal domain of the actinomycetal Nei2 and related DNA glycosylases; This family contains ...
 1-79 5.98e-09

N-terminal domain of the actinomycetal Nei2 and related DNA glycosylases; This family contains the N-terminal domain of the actinomycetal Nei2 and related DNA glycosylases. It belongs to the FpgNei_N, [N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII)] domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. They initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycosylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. This family contains mostly actinomycetes and includes Mycobacterium tuberculosis Nei2 (MtuNei2). Complementation experiments in repair-deficient Escherichia coli (fpg mutY nei triple and nei nth double mutants), support that MtuNei2 is functionally active in vivo and recognizes both guanine and cytosine oxidation products. In addition to this AcNei2_N domain, enzymes belonging to this family contain a helix-two turn-helix (H2TH) domain and a zinc-finger motif.


Pssm-ID: 176805  Cd Length: 114  Bit Score: 52.97  E-value: 5.98e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1498198564   1 MPELPEVETVARSLAPQLQGRTITGlAKLDWPKMLTpspdefaALIAGRRIEAIGRRAKWLLLSLDGEWTLAIHLRMSG 79
Cdd:cd08971     1 MPEGDTVHRAARRLRRALAGRVLTR-ADLRVPRLAT-------ADLAGRTVEEVVARGKHLLIRFDGGLTLHTHLRMDG 71
RqcH COG1293
Ribosome quality control (RQC) protein RqcH, Rqc2/NEMF/Tae2 family, contains fibronectin-(FbpA) ...
 136-216 6.93e-06

Ribosome quality control (RQC) protein RqcH, Rqc2/NEMF/Tae2 family, contains fibronectin-(FbpA) and RNA- (NFACT) binding domains [Translation, ribosomal structure and biogenesis, Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440904 [Multi-domain]  Cd Length: 578  Bit Score: 47.14  E-value: 6.93e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1498198564 136 PLaaDFTPSALAERLQNRRAPIKALLLDQhlIAGIGNIYANEALWLARIHPLTPGAMLTPEQINELHHAIRHVLQEAITN 215
Cdd:COG1293   172 PL--ELSEEEFAELLSESDGDLVRTLATN--FLGLSPLLAEEICYRAGLDKDTPTDELSEEDLEALYEALQELLEELENG 247


                  .
gi 1498198564 216 Q 216
Cdd:COG1293   248 E 248
BaFpgNei_N_3 cd08975
Uncharacterized bacterial subgroup of the N-terminal domain of Fpg (formamidopyrimidine-DNA ...
 3-54 4.45e-03

Uncharacterized bacterial subgroup of the N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) base-excision repair DNA glycosylases; This family is an uncharacterized bacterial subgroup of the FpgNei_N domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. They initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycosylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. One exception is mouse Nei-like glycosylase 3 (Neil3) which forms a Schiff base intermediate via its N-terminal valine. In this family the N-terminal proline is replaced by an isoleucine or valine. Escherichia coli Fpg prefers 8-oxo-7,8-dihydroguanine (8-oxoG) and oxidized purines and Escherichia coli Nei recognizes oxidized pyrimidines. However, neither Escherichia coli Fpg or Nei belong to this family. In addition to this BaFpgNei_N_3 domain, enzymes belonging to this family contain a helix-two turn-helix (H2TH) domain and a zinc-finger motif.


Pssm-ID: 176809  Cd Length: 117  Bit Score: 36.15  E-value: 4.45e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1498198564   3 ELPEVETVARSLAPQLQGRTITGLakldWPKMlTP--------SPDEFAALIAGRRIEAI 54
Cdd:cd08975     2 ELPESATLSKQLNETLKGKRITDV----FPAT-SPhkftwyngDPNEYDELLVGKRITSA 56
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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